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- PDB-4ue9: Complex of D. melanogaster eIF4E with the 4E-binding protein 4E-T -

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Basic information

Entry
Database: PDB / ID: 4ue9
TitleComplex of D. melanogaster eIF4E with the 4E-binding protein 4E-T
Components
  • EUKARYOTIC TRANSLATION INITIATION FACTOR 4E
  • EUKARYOTIC TRANSLATION INITIATION FACTOR 4E TRANSPORTER
KeywordsTRANSLATION / GENE REGULATION / CAP BINDING PROTEIN / 4E BINDING PROTEIN / TRANSLATIONAL REPRESSION
Function / homology
Function and homology information


negative regulation of eukaryotic translation initiation factor 4F complex assembly / TOR signaling pathway / Activation of the mRNA upon binding of the cap-binding complex and eIFs, and subsequent binding to 43S / Transport of the SLBP independent Mature mRNA / Transport of the SLBP Dependant Mature mRNA / Transport of Mature mRNA Derived from an Intronless Transcript / ISG15 antiviral mechanism / L13a-mediated translational silencing of Ceruloplasmin expression / mTORC1-mediated signalling / Translation initiation complex formation ...negative regulation of eukaryotic translation initiation factor 4F complex assembly / TOR signaling pathway / Activation of the mRNA upon binding of the cap-binding complex and eIFs, and subsequent binding to 43S / Transport of the SLBP independent Mature mRNA / Transport of the SLBP Dependant Mature mRNA / Transport of Mature mRNA Derived from an Intronless Transcript / ISG15 antiviral mechanism / L13a-mediated translational silencing of Ceruloplasmin expression / mTORC1-mediated signalling / Translation initiation complex formation / Ribosomal scanning and start codon recognition / muscle cell postsynaptic specialization / RNA metabolic process / neuronal ribonucleoprotein granule / eukaryotic initiation factor 4G binding / eukaryotic initiation factor 4E binding / RNA cap binding / eukaryotic translation initiation factor 4F complex / RNA 7-methylguanosine cap binding / translation initiation factor activity / neuromuscular junction / translational initiation / P-body / regulation of translation / negative regulation of translation / nuclear body / translation / mRNA binding / nucleus / cytoplasm / cytosol
Similarity search - Function
Eukaryotic translation initiation factor 4E binding protein / Nucleocytoplasmic shuttling protein for mRNA cap-binding EIF4E / RNA Cap, Translation Initiation Factor Eif4e / RNA Cap, Translation Initiation Factor Eif4e / Eukaryotic translation initiation factor 4E (eIF-4E), conserved site / Eukaryotic initiation factor 4E signature. / Translation Initiation factor eIF- 4e / Eukaryotic initiation factor 4E / Translation Initiation factor eIF- 4e-like / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Eukaryotic translation initiation factor 4E1 / Eukaryotic translation initiation factor 4E transporter
Similarity search - Component
Biological speciesDROSOPHILA MELANOGASTER (fruit fly)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 Å
AuthorsPeter, D. / Weichenrieder, O.
CitationJournal: Mol.Cell / Year: 2015
Title: Molecular Architecture of 4E-BP Translational Inhibitors Bound to Eif4E.
Authors: Peter, D. / Igreja, C. / Weber, R. / Wohlbold, L. / Weiler, C. / Ebertsch, L. / Weichenrieder, O. / Izaurralde, E.
History
DepositionDec 16, 2014Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 25, 2015Provider: repository / Type: Initial release
Revision 1.1Mar 4, 2015Group: Database references
Revision 1.2Apr 15, 2015Group: Database references
Revision 1.3Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf
Remark 650 HELIX DETERMINATION METHOD: AUTHOR PROVIDED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: EUKARYOTIC TRANSLATION INITIATION FACTOR 4E
B: EUKARYOTIC TRANSLATION INITIATION FACTOR 4E TRANSPORTER


Theoretical massNumber of molelcules
Total (without water)26,0222
Polymers26,0222
Non-polymers00
Water68538
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2730 Å2
ΔGint-12.8 kcal/mol
Surface area11160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)40.000, 40.000, 443.060
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522

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Components

#1: Protein EUKARYOTIC TRANSLATION INITIATION FACTOR 4E / EIF4E / EIF-4F 25 KDA SUBUNIT / MRNA CAP-BINDING PROTEIN


Mass: 21249.037 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 80-259
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) DROSOPHILA MELANOGASTER (fruit fly) / Plasmid: PETMCN (PNEA) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): STAR / References: UniProt: P48598
#2: Protein/peptide EUKARYOTIC TRANSLATION INITIATION FACTOR 4E TRANSPORTER


Mass: 4772.581 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 9-44
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) DROSOPHILA MELANOGASTER (fruit fly) / Plasmid: PETMCN (PNEA) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): STAR / References: UniProt: Q8IH18
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 38 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE FIRST FOUR RESIDUES OF CHAIN A REMAIN FROM THE EXPRESSION TAG. COMPARED TO UNP P48598, SEQUENCE ...THE FIRST FOUR RESIDUES OF CHAIN A REMAIN FROM THE EXPRESSION TAG. COMPARED TO UNP P48598, SEQUENCE NUMBERS OF CHAIN A ARE SHIFTED BY -11 RESIDUES. NUMBERING CORRESPONDS TO UNP P48598-2 AND PDB 4AXG. THE FIRST FOUR RESIDUES OF CHAIN B REMAIN FROM THE EXPRESSION TAG.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.1 Å3/Da / Density % sol: 41 % / Description: NONE
Crystal growpH: 8.5 / Details: 0.1M TRIS-HCL PH 8.5, 0.05M LISO4, 28% PEG400

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 6, 2014 / Details: DYNAMICALLY BENDABLE MIRRORS
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.15→36.9 Å / Num. obs: 12812 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 34.7 % / Biso Wilson estimate: 43.25 Å2 / Rsym value: 0.09 / Net I/σ(I): 25.6
Reflection shellResolution: 2.15→2.21 Å / Redundancy: 31.4 % / Mean I/σ(I) obs: 4.5 / Rsym value: 0.71 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE: 1.9_1692)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4UE8 CHAIN A

4ue8


Resolution: 2.15→36.922 Å / SU ML: 0.25 / σ(F): 1.4 / Phase error: 27.88 / Stereochemistry target values: ML
Details: HYDROGENS WERE REFINED IN THE RIDING POSITIONS. THE SIDECHAINS OF THE FOLLOWING RESIDUES WERE TRUNCATED AT C-BETA ATOMS. CHAIN A, RESIDUES 88, 89. CHAIN B, RESIDUES 25, 29, 33. THE FOLLOWING ...Details: HYDROGENS WERE REFINED IN THE RIDING POSITIONS. THE SIDECHAINS OF THE FOLLOWING RESIDUES WERE TRUNCATED AT C-BETA ATOMS. CHAIN A, RESIDUES 88, 89. CHAIN B, RESIDUES 25, 29, 33. THE FOLLOWING RESIDUES ARE DISORDERED. CHAIN A, RESIDUES 86 TO 87, 237 TO 240. CHAIN B, RESIDUES 26 TO 28.
RfactorNum. reflection% reflection
Rfree0.2714 676 5.3 %
Rwork0.2354 --
obs0.2374 12796 99.88 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 50.03 Å2
Refinement stepCycle: LAST / Resolution: 2.15→36.922 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1701 0 0 38 1739
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0021735
X-RAY DIFFRACTIONf_angle_d0.5642343
X-RAY DIFFRACTIONf_dihedral_angle_d11.512635
X-RAY DIFFRACTIONf_chiral_restr0.025257
X-RAY DIFFRACTIONf_plane_restr0.001294
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1503-2.31630.30921300.24622326X-RAY DIFFRACTION100
2.3163-2.54930.35481250.26742322X-RAY DIFFRACTION100
2.5493-2.91810.34471370.27112371X-RAY DIFFRACTION100
2.9181-3.6760.27831250.24522438X-RAY DIFFRACTION100
3.676-36.92710.23441590.21522663X-RAY DIFFRACTION100

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